Starting phenix.real_space_refine on Mon Jun 24 17:40:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx5_37901/06_2024/8wx5_37901.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx5_37901/06_2024/8wx5_37901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx5_37901/06_2024/8wx5_37901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx5_37901/06_2024/8wx5_37901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx5_37901/06_2024/8wx5_37901.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx5_37901/06_2024/8wx5_37901.pdb" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2552 2.51 5 N 619 2.21 5 O 664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 523": "OD1" <-> "OD2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3857 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3741 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 22, 'TRANS': 467} Chain breaks: 1 Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Time building chain proxies: 3.05, per 1000 atoms: 0.79 Number of scatterers: 3857 At special positions: 0 Unit cell: (80.51, 77.19, 73.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 664 8.00 N 619 7.00 C 2552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 152 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 725.1 milliseconds 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 922 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 83.7% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 28 through 57 removed outlier: 3.927A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.539A pdb=" N ASN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 97 Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 101 through 125 Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 146 through 185 removed outlier: 3.514A pdb=" N ALA A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Proline residue: A 155 - end of helix removed outlier: 4.443A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 4.049A pdb=" N ASP A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 220 Processing helix chain 'A' and resid 221 through 245 Proline residue: A 229 - end of helix removed outlier: 4.111A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 310 through 349 Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix Processing helix chain 'A' and resid 354 through 358 removed outlier: 4.283A pdb=" N ILE A 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 394 Proline residue: A 382 - end of helix Proline residue: A 390 - end of helix removed outlier: 3.897A pdb=" N ARG A 394 " --> pdb=" O PRO A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 431 Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 453 through 479 removed outlier: 4.550A pdb=" N GLN A 457 " --> pdb=" O TRP A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 512 Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 531 through 556 removed outlier: 4.067A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 14 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 437 removed outlier: 3.715A pdb=" N GLN A 437 " --> pdb=" O TYR A 444 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 588 1.31 - 1.43: 1104 1.43 - 1.56: 2230 1.56 - 1.69: 0 1.69 - 1.82: 33 Bond restraints: 3955 Sorted by residual: bond pdb=" C SER B 8 " pdb=" O SER B 8 " ideal model delta sigma weight residual 1.236 1.307 -0.070 1.24e-02 6.50e+03 3.21e+01 bond pdb=" C LEU B 7 " pdb=" O LEU B 7 " ideal model delta sigma weight residual 1.236 1.294 -0.058 1.19e-02 7.06e+03 2.34e+01 bond pdb=" CA SER B 8 " pdb=" CB SER B 8 " ideal model delta sigma weight residual 1.530 1.452 0.078 1.69e-02 3.50e+03 2.11e+01 bond pdb=" C TYR B 6 " pdb=" O TYR B 6 " ideal model delta sigma weight residual 1.235 1.181 0.054 1.26e-02 6.30e+03 1.84e+01 bond pdb=" C GLY B 9 " pdb=" O GLY B 9 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.35e-02 5.49e+03 1.72e+01 ... (remaining 3950 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.25: 132 107.25 - 114.04: 2237 114.04 - 120.83: 1887 120.83 - 127.62: 1091 127.62 - 134.42: 37 Bond angle restraints: 5384 Sorted by residual: angle pdb=" N GLU B 4 " pdb=" CA GLU B 4 " pdb=" C GLU B 4 " ideal model delta sigma weight residual 112.34 102.39 9.95 1.30e+00 5.92e-01 5.86e+01 angle pdb=" N LEU B 10 " pdb=" CA LEU B 10 " pdb=" C LEU B 10 " ideal model delta sigma weight residual 111.37 100.45 10.92 1.64e+00 3.72e-01 4.43e+01 angle pdb=" N TRP B 13 " pdb=" CA TRP B 13 " pdb=" C TRP B 13 " ideal model delta sigma weight residual 111.37 102.04 9.33 1.65e+00 3.67e-01 3.20e+01 angle pdb=" N SER B 8 " pdb=" CA SER B 8 " pdb=" C SER B 8 " ideal model delta sigma weight residual 111.75 104.52 7.23 1.28e+00 6.10e-01 3.19e+01 angle pdb=" N TYR B 12 " pdb=" CA TYR B 12 " pdb=" C TYR B 12 " ideal model delta sigma weight residual 111.36 117.06 -5.70 1.09e+00 8.42e-01 2.73e+01 ... (remaining 5379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 2037 17.98 - 35.95: 206 35.95 - 53.93: 43 53.93 - 71.91: 3 71.91 - 89.89: 2 Dihedral angle restraints: 2291 sinusoidal: 849 harmonic: 1442 Sorted by residual: dihedral pdb=" N SER B 8 " pdb=" C SER B 8 " pdb=" CA SER B 8 " pdb=" CB SER B 8 " ideal model delta harmonic sigma weight residual 122.80 112.32 10.48 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" N LEU B 10 " pdb=" C LEU B 10 " pdb=" CA LEU B 10 " pdb=" CB LEU B 10 " ideal model delta harmonic sigma weight residual 122.80 112.37 10.43 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" C TRP B 13 " pdb=" N TRP B 13 " pdb=" CA TRP B 13 " pdb=" CB TRP B 13 " ideal model delta harmonic sigma weight residual -122.60 -113.16 -9.44 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 2288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 564 0.064 - 0.128: 57 0.128 - 0.192: 3 0.192 - 0.256: 1 0.256 - 0.319: 3 Chirality restraints: 628 Sorted by residual: chirality pdb=" CA TRP B 13 " pdb=" N TRP B 13 " pdb=" C TRP B 13 " pdb=" CB TRP B 13 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA TYR B 12 " pdb=" N TYR B 12 " pdb=" C TYR B 12 " pdb=" CB TYR B 12 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA LEU B 10 " pdb=" N LEU B 10 " pdb=" C LEU B 10 " pdb=" CB LEU B 10 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 625 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 9 " 0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C GLY B 9 " -0.071 2.00e-02 2.50e+03 pdb=" O GLY B 9 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU B 10 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 10 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.99e+00 pdb=" C LEU B 10 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU B 10 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU B 11 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 228 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A 229 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " -0.029 5.00e-02 4.00e+02 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 215 2.73 - 3.27: 4249 3.27 - 3.81: 6741 3.81 - 4.36: 7416 4.36 - 4.90: 12796 Nonbonded interactions: 31417 Sorted by model distance: nonbonded pdb=" O LEU A 349 " pdb=" NE2 GLN A 437 " model vdw 2.184 2.520 nonbonded pdb=" O GLN A 337 " pdb=" OG1 THR A 341 " model vdw 2.200 2.440 nonbonded pdb=" OG SER A 355 " pdb=" O THR A 358 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR A 333 " pdb=" O GLY A 499 " model vdw 2.259 2.440 nonbonded pdb=" O LEU A 380 " pdb=" N LYS A 384 " model vdw 2.280 2.520 ... (remaining 31412 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.450 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.710 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 3955 Z= 0.255 Angle : 0.867 10.916 5384 Z= 0.555 Chirality : 0.044 0.319 628 Planarity : 0.005 0.051 664 Dihedral : 14.579 89.886 1363 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.63 % Favored : 92.97 % Rotamer: Outliers : 0.50 % Allowed : 6.98 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.34), residues: 498 helix: -0.26 (0.24), residues: 389 sheet: -4.91 (0.87), residues: 10 loop : -4.00 (0.45), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 13 HIS 0.002 0.000 HIS A 362 PHE 0.012 0.001 PHE A 67 TYR 0.022 0.002 TYR B 12 ARG 0.001 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.9316 (mt) cc_final: 0.9044 (mt) REVERT: A 63 ASN cc_start: 0.7813 (m110) cc_final: 0.7512 (t0) REVERT: A 259 ASP cc_start: 0.9094 (m-30) cc_final: 0.8872 (m-30) REVERT: A 310 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8282 (mm-30) REVERT: A 409 MET cc_start: 0.9073 (mtt) cc_final: 0.8799 (mtt) REVERT: A 453 TRP cc_start: 0.7998 (m100) cc_final: 0.7208 (m100) REVERT: A 465 GLU cc_start: 0.9358 (tp30) cc_final: 0.9097 (tp30) REVERT: A 470 ILE cc_start: 0.8834 (mm) cc_final: 0.8583 (mm) REVERT: A 474 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7222 (mt-10) outliers start: 2 outliers final: 1 residues processed: 158 average time/residue: 0.1327 time to fit residues: 26.5528 Evaluate side-chains 129 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN A 356 ASN A 441 ASN A 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3955 Z= 0.201 Angle : 0.644 8.037 5384 Z= 0.330 Chirality : 0.040 0.172 628 Planarity : 0.005 0.051 664 Dihedral : 4.642 15.979 538 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.24 % Allowed : 15.46 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.38), residues: 498 helix: 0.89 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -3.33 (0.49), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 13 HIS 0.002 0.001 HIS A 348 PHE 0.017 0.001 PHE A 194 TYR 0.035 0.002 TYR B 12 ARG 0.007 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9542 (mt) cc_final: 0.9129 (mp) REVERT: A 120 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8277 (t80) REVERT: A 129 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7824 (ttm110) REVERT: A 259 ASP cc_start: 0.9104 (m-30) cc_final: 0.8885 (m-30) REVERT: A 409 MET cc_start: 0.9151 (mtt) cc_final: 0.8766 (mtt) REVERT: A 423 GLU cc_start: 0.8444 (tp30) cc_final: 0.8126 (tp30) REVERT: A 426 ARG cc_start: 0.8763 (ttp80) cc_final: 0.8554 (ttp80) REVERT: A 453 TRP cc_start: 0.8127 (m100) cc_final: 0.7423 (m100) REVERT: A 465 GLU cc_start: 0.9365 (tp30) cc_final: 0.8970 (tp30) REVERT: A 470 ILE cc_start: 0.8827 (mm) cc_final: 0.8541 (mm) REVERT: A 474 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7344 (mt-10) REVERT: A 501 PHE cc_start: 0.8586 (m-80) cc_final: 0.7575 (t80) REVERT: A 543 GLN cc_start: 0.9487 (tp40) cc_final: 0.8969 (tp-100) REVERT: B 13 TRP cc_start: 0.5921 (OUTLIER) cc_final: 0.4621 (t-100) outliers start: 17 outliers final: 8 residues processed: 144 average time/residue: 0.1194 time to fit residues: 22.6034 Evaluate side-chains 133 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3955 Z= 0.204 Angle : 0.641 8.085 5384 Z= 0.327 Chirality : 0.041 0.162 628 Planarity : 0.005 0.052 664 Dihedral : 4.614 16.718 537 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.74 % Allowed : 20.95 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.39), residues: 498 helix: 1.24 (0.27), residues: 390 sheet: None (None), residues: 0 loop : -2.97 (0.54), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 13 HIS 0.002 0.001 HIS A 348 PHE 0.012 0.001 PHE A 195 TYR 0.028 0.002 TYR B 12 ARG 0.006 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9539 (mt) cc_final: 0.9138 (mp) REVERT: A 69 TRP cc_start: 0.8958 (m-10) cc_final: 0.8554 (m-10) REVERT: A 259 ASP cc_start: 0.9106 (m-30) cc_final: 0.8894 (m-30) REVERT: A 310 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8700 (mm-30) REVERT: A 409 MET cc_start: 0.9153 (mtt) cc_final: 0.8863 (mtt) REVERT: A 426 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8494 (ttp80) REVERT: A 453 TRP cc_start: 0.8152 (m100) cc_final: 0.7423 (m100) REVERT: A 465 GLU cc_start: 0.9331 (tp30) cc_final: 0.8969 (tp30) REVERT: A 470 ILE cc_start: 0.8757 (mm) cc_final: 0.8437 (mm) REVERT: A 474 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7384 (mt-10) REVERT: A 501 PHE cc_start: 0.8643 (m-80) cc_final: 0.7649 (t80) outliers start: 15 outliers final: 11 residues processed: 132 average time/residue: 0.1222 time to fit residues: 21.3640 Evaluate side-chains 132 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3955 Z= 0.220 Angle : 0.627 9.288 5384 Z= 0.323 Chirality : 0.040 0.133 628 Planarity : 0.005 0.050 664 Dihedral : 4.550 17.386 537 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.74 % Allowed : 24.69 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.39), residues: 498 helix: 1.31 (0.26), residues: 396 sheet: None (None), residues: 0 loop : -2.65 (0.63), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 13 HIS 0.002 0.001 HIS A 348 PHE 0.013 0.001 PHE A 194 TYR 0.027 0.002 TYR B 12 ARG 0.006 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 ASP cc_start: 0.9130 (m-30) cc_final: 0.8928 (m-30) REVERT: A 316 LYS cc_start: 0.8904 (tttt) cc_final: 0.8678 (ttmt) REVERT: A 426 ARG cc_start: 0.8771 (ttp80) cc_final: 0.8416 (ttp80) REVERT: A 453 TRP cc_start: 0.8211 (m100) cc_final: 0.7498 (m100) REVERT: A 470 ILE cc_start: 0.8773 (mm) cc_final: 0.8433 (mm) REVERT: A 474 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 501 PHE cc_start: 0.8659 (m-80) cc_final: 0.7722 (t80) REVERT: B 13 TRP cc_start: 0.5884 (OUTLIER) cc_final: 0.4557 (t-100) outliers start: 19 outliers final: 12 residues processed: 134 average time/residue: 0.1147 time to fit residues: 20.1648 Evaluate side-chains 135 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 3955 Z= 0.417 Angle : 0.762 9.992 5384 Z= 0.399 Chirality : 0.044 0.155 628 Planarity : 0.005 0.046 664 Dihedral : 4.724 21.216 537 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 5.24 % Allowed : 26.93 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.38), residues: 498 helix: 0.99 (0.25), residues: 394 sheet: None (None), residues: 0 loop : -2.68 (0.63), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 13 HIS 0.003 0.001 HIS A 348 PHE 0.017 0.002 PHE A 411 TYR 0.020 0.003 TYR B 12 ARG 0.004 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.8709 (mmm) cc_final: 0.8275 (tpp) REVERT: A 259 ASP cc_start: 0.9158 (m-30) cc_final: 0.8952 (m-30) REVERT: A 310 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8582 (mm-30) REVERT: A 316 LYS cc_start: 0.8947 (tttt) cc_final: 0.8745 (ttmt) REVERT: A 417 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8478 (t80) REVERT: A 474 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7494 (mt-10) outliers start: 21 outliers final: 15 residues processed: 137 average time/residue: 0.1283 time to fit residues: 22.3392 Evaluate side-chains 136 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 502 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.0030 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3955 Z= 0.211 Angle : 0.663 6.927 5384 Z= 0.340 Chirality : 0.041 0.136 628 Planarity : 0.005 0.047 664 Dihedral : 4.651 18.675 537 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.24 % Allowed : 30.92 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.39), residues: 498 helix: 1.26 (0.26), residues: 396 sheet: None (None), residues: 0 loop : -2.43 (0.68), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 13 HIS 0.002 0.001 HIS A 348 PHE 0.011 0.001 PHE A 67 TYR 0.025 0.002 TYR B 12 ARG 0.007 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.8580 (mmm) cc_final: 0.8220 (tpp) REVERT: A 259 ASP cc_start: 0.9092 (m-30) cc_final: 0.8873 (m-30) REVERT: A 310 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8526 (mm-30) REVERT: A 316 LYS cc_start: 0.8892 (tttt) cc_final: 0.8682 (ttmt) REVERT: A 417 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8402 (t80) REVERT: A 453 TRP cc_start: 0.8245 (m100) cc_final: 0.7401 (m100) REVERT: A 465 GLU cc_start: 0.9307 (tp30) cc_final: 0.9012 (tp30) REVERT: A 474 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7435 (mt-10) REVERT: A 501 PHE cc_start: 0.8748 (m-80) cc_final: 0.7781 (t80) REVERT: B 13 TRP cc_start: 0.5869 (OUTLIER) cc_final: 0.4720 (t-100) outliers start: 13 outliers final: 9 residues processed: 136 average time/residue: 0.1266 time to fit residues: 21.9975 Evaluate side-chains 135 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.0060 chunk 32 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3955 Z= 0.207 Angle : 0.658 6.524 5384 Z= 0.340 Chirality : 0.041 0.141 628 Planarity : 0.005 0.047 664 Dihedral : 4.603 17.805 537 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.49 % Allowed : 32.17 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.39), residues: 498 helix: 1.32 (0.26), residues: 396 sheet: None (None), residues: 0 loop : -2.25 (0.69), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 13 HIS 0.001 0.000 HIS A 348 PHE 0.015 0.001 PHE A 240 TYR 0.034 0.002 TYR A 535 ARG 0.008 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.8548 (mmm) cc_final: 0.8189 (tpp) REVERT: A 259 ASP cc_start: 0.9076 (m-30) cc_final: 0.8859 (m-30) REVERT: A 310 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8634 (mm-30) REVERT: A 384 LYS cc_start: 0.8881 (pptt) cc_final: 0.8604 (pptt) REVERT: A 417 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8386 (t80) REVERT: A 423 GLU cc_start: 0.8530 (tp30) cc_final: 0.8109 (tp30) REVERT: A 453 TRP cc_start: 0.8245 (m100) cc_final: 0.7530 (m100) REVERT: A 474 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7506 (mt-10) REVERT: A 501 PHE cc_start: 0.8703 (m-80) cc_final: 0.7675 (t80) REVERT: B 13 TRP cc_start: 0.5742 (OUTLIER) cc_final: 0.4246 (t-100) outliers start: 14 outliers final: 10 residues processed: 132 average time/residue: 0.1161 time to fit residues: 19.9891 Evaluate side-chains 137 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3955 Z= 0.209 Angle : 0.650 6.466 5384 Z= 0.335 Chirality : 0.040 0.133 628 Planarity : 0.005 0.048 664 Dihedral : 4.552 17.620 537 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.74 % Allowed : 32.42 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.39), residues: 498 helix: 1.33 (0.26), residues: 396 sheet: None (None), residues: 0 loop : -2.13 (0.67), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 13 HIS 0.001 0.000 HIS A 348 PHE 0.013 0.001 PHE A 494 TYR 0.024 0.002 TYR A 535 ARG 0.010 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.8547 (mmm) cc_final: 0.8187 (tpp) REVERT: A 259 ASP cc_start: 0.9061 (m-30) cc_final: 0.8844 (m-30) REVERT: A 310 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8691 (mm-30) REVERT: A 384 LYS cc_start: 0.8865 (pptt) cc_final: 0.8577 (pptt) REVERT: A 417 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8373 (t80) REVERT: A 423 GLU cc_start: 0.8367 (tp30) cc_final: 0.8147 (tp30) REVERT: A 453 TRP cc_start: 0.8232 (m100) cc_final: 0.7541 (m100) REVERT: A 474 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7487 (mt-10) REVERT: A 501 PHE cc_start: 0.8666 (m-80) cc_final: 0.7690 (t80) REVERT: B 13 TRP cc_start: 0.5713 (OUTLIER) cc_final: 0.4951 (m100) outliers start: 11 outliers final: 9 residues processed: 135 average time/residue: 0.1181 time to fit residues: 20.7564 Evaluate side-chains 139 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 0.0670 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3955 Z= 0.200 Angle : 0.650 7.037 5384 Z= 0.335 Chirality : 0.040 0.135 628 Planarity : 0.005 0.048 664 Dihedral : 4.536 17.363 537 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.49 % Allowed : 33.67 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.39), residues: 498 helix: 1.31 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -2.14 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 13 HIS 0.001 0.000 HIS A 348 PHE 0.011 0.001 PHE A 237 TYR 0.023 0.002 TYR B 12 ARG 0.010 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.8520 (mmm) cc_final: 0.8170 (tpp) REVERT: A 259 ASP cc_start: 0.9035 (m-30) cc_final: 0.8830 (m-30) REVERT: A 384 LYS cc_start: 0.8805 (pptt) cc_final: 0.8545 (pptt) REVERT: A 453 TRP cc_start: 0.8206 (m100) cc_final: 0.7525 (m100) REVERT: A 465 GLU cc_start: 0.9296 (tp30) cc_final: 0.8932 (tp30) REVERT: A 474 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 501 PHE cc_start: 0.8680 (m-80) cc_final: 0.7664 (t80) REVERT: B 13 TRP cc_start: 0.5667 (OUTLIER) cc_final: 0.5086 (m100) outliers start: 10 outliers final: 8 residues processed: 130 average time/residue: 0.1163 time to fit residues: 19.6835 Evaluate side-chains 131 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN A 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3955 Z= 0.206 Angle : 0.645 6.852 5384 Z= 0.333 Chirality : 0.040 0.135 628 Planarity : 0.005 0.047 664 Dihedral : 4.496 17.417 537 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.24 % Allowed : 33.42 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.39), residues: 498 helix: 1.35 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -2.11 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 13 HIS 0.001 0.000 HIS A 348 PHE 0.011 0.001 PHE A 198 TYR 0.021 0.002 TYR B 12 ARG 0.008 0.000 ARG A 426 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.8529 (mmm) cc_final: 0.8201 (tpp) REVERT: A 259 ASP cc_start: 0.9037 (m-30) cc_final: 0.8830 (m-30) REVERT: A 384 LYS cc_start: 0.8744 (pptt) cc_final: 0.8523 (pptt) REVERT: A 453 TRP cc_start: 0.8205 (m100) cc_final: 0.7544 (m100) REVERT: A 465 GLU cc_start: 0.9319 (tp30) cc_final: 0.8970 (tp30) REVERT: A 474 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7411 (mt-10) REVERT: A 501 PHE cc_start: 0.8684 (m-80) cc_final: 0.7667 (t80) REVERT: B 13 TRP cc_start: 0.5602 (OUTLIER) cc_final: 0.4968 (m100) outliers start: 9 outliers final: 8 residues processed: 126 average time/residue: 0.1090 time to fit residues: 18.0675 Evaluate side-chains 131 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain B residue 13 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 0.0050 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120340 restraints weight = 7583.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.124150 restraints weight = 4277.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.126805 restraints weight = 2872.841| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3955 Z= 0.202 Angle : 0.643 7.112 5384 Z= 0.332 Chirality : 0.040 0.135 628 Planarity : 0.005 0.047 664 Dihedral : 4.502 17.325 537 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.24 % Allowed : 33.42 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.39), residues: 498 helix: 1.37 (0.26), residues: 398 sheet: -1.51 (1.71), residues: 10 loop : -2.05 (0.70), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 13 HIS 0.001 0.000 HIS A 348 PHE 0.011 0.001 PHE A 237 TYR 0.021 0.002 TYR B 12 ARG 0.008 0.000 ARG A 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1215.38 seconds wall clock time: 22 minutes 34.52 seconds (1354.52 seconds total)